LESSON 14: The Future of Y Testing is Here

Advances in science and technology have closed the gap between the genealogical time frame of Y-STR markers and what used to be considered the deep ancestry or ancient Y-SNPS. We now can identify YSNPS that may have happened only a generation or two ago and literally climb our way back up the Y Haplotree to the earliest YDNA Halplogroups. To give you an idea of the changes in price in Next Generation Y testing, in October 2015 the Full Genomes product Y Elite was $750 (down from an early price of $1200). Price on the Big Y from FTDNA was $575. Now in September of 2020 the cost of a Y Elite is $425 and a Big Y 700 is now $449 (does not include Raw data fie which is an additional charge). In 2002 the Y Tree has about 245 YSNPS and 153 branches. By the advent of Next Generation tetsing we we reached 6,556 SNPS in 2015 and by 2016 13,767. In the Fall of 2020 we are looking at about 302,000 YSNPS and 33,000 branches of the Y tree. A veritable explosion in testing! Nearly a 900 fold increase in SNPS. This has been made possible by Next Generation testing, the drop in price and wide scale testing. Not only does this help us follow the paths of various branches over time it allows us to bridge the gap making YSNPS relevant in a genealogical time frame.

YearSNPSBranches
2002245153
2006436
2008790
2010935
20133,610
20156,556
2016 Big Y23,767
201872,166
April 2019149,200
June 2019161,341

September 2019178,892
April 2020220,00027,000
September2020302,00033,000
YSNP Explosion

In this lesson I hope to explain what comprehensive Y testing means to the average genetic genealogist. Anyone using DNA for genealogical purposes is a genetic genealogist but the range of how far one delves into DNA testing varies from those taking a 37 marker Y test to those testing mtDNA, YDNA and atDNA at multiple companies. For this lesson I want to talk about the practical application of advanced Y-DNA SNP testing. The International Society of Genetic Genealogists (ISOGG) maintains a SNP index and the Y Haplogroup Tree, however because new SNPS are being found daily the most comprehensive information is often within Haplogroup projects and Surname projects and their administrators are the best source of current information. In addition FTDNA maintains a Y Haplotree and a mtDNA Haplotree that are public, as does YFULL. YFULL and Full Genomes Corporation offer $49 NextGen Sequence Interpretation. If you are a member of Haplogroup R-P312 Y-DNA interpretation is available through Alex WIlliamson’s Big Tree at no cost if you upload your results.

FGC22501 Branch of The Big Tree

COMPREHENSIVE Y-SNP TESTING

It is imperative to understand what these new advances mean in order to make good decisions on whether to purchase additional tests and if so which tests and when to purchase them. Without going further I can say without equivocation that early adopters of nearly every DNA product have helped all that test later. In many cases they paid far more than those that tested a few years later as technology has made DNA testing increasingly more refined and more affordable. In some cases these tests proved quite helpful to an individual or group of individuals and sometimes they were a complete bust. Early testers with the CHROMO 2.0, GENO 2, and Big Y are no exception, depending on your specific situation and how well tested your branch of the Y-tree.

The Elite Y tests all areas of the Y that current technology is able to extract and includes YSNPS, YSTRS and mtDNA. The Big Y 700 from FTDNA tests a smaller subset of Y-SNPS but far more than the earlier Big Y 500. Both have  proved helpful in expanding the Y Haplotree. The Big Y has the advantage of more testers and an easier to use platform. Y Elite has broader coverage and includes the RAW Data and mtDNA. They both include YSTRS.

If you cannot afford one of these products work with others in your surname project to sponsor a test or two. Then spot testing of individuals can be cost effective but alas less comprehenisve. If you have not already done so join your Haplogroup Project and work with Project Administrators on further testing. Also work with your Surname Project Administrator. It is not necessary for you to be the test subject to benefit. If you are descended from a common ancestor and you are a match via STR markers you will most likely share all but a few SNPS with another member of your Surname Group. Spot testing can confirm exactly where. 

One of the major by products of these early NGS tests has been the discovery of new SNPS that others are able to test via lower cost fixed panels or singletons. This is a less expensive alternative to a Big Y or Y Elite. Panel can range from $89-$239 depending on the panel and number of SNPS. A SNP test costs $38 at FTDNA and $18 (= one time kit fee of $5) at YSEQ.net. The panels are available at FTDA tend to be Haplogroup panels and at YSEQ there are many custom panels at. As in most genetic testing it is often easy to convince people to test at a lower price point even if they eventually test further making the cumulative cost greater. All Haplogroups and subgroups are different. Even as I write this some are well tested and others not so much. Those in very common Haplogroups may more easily depend on others for testing than those in less common ones.

The major benefit of the Big Y test (from FTDNA) or the more comprehensive Elite Y (from FGC) is that they will discover and define the Y Haplogroup tree to the point that private SNPs will define families or parts of families. Until the advent of Next generation sequencing (Big Y and Y Elite) Y-STRS were the way to go for recent genealogy and Y-SNPs were used for ancient or genealogy back thousands of years. These new tests, by uncovering thousands and thousands of new SNPS are bridging the time gap and map the Y Tree with ever finer detail. The new tests are primarily testing YSNPS, although the YSTRS are included. One advantage SNPS have over STRS is that they happen only once (with very rare exceptions). So that everyone sharing a particular Y-SNP shares a common ancestor. In the past these SNPS represented mutations that happened thousands of years ago but new technology is bringing us SNPS that have happened in the past 50-500 years. Many of these SNPS are considered private or semi-private. What this means is that when a new Y-SNP is discovered it will be considered private if it does not appear in any other samples and semi-private if it appears in a small number of samples with the same surname or a low Genetic Distance.

If we compare Y-SNPS with Y-STRS the latter change with much greater frequency and represent the number of repeats at a given marker. They may pick up or drop off a repeat every now and then. YSTRS do not represent  one time events. It is possible that a grandfather might have 24 repeats and his grandson 23 repeats at a given marker and then down the line a ggg-grandson has 24 or 22. With a YSNP every man bearing a particular SNP inherited it from the same man whether that common ancestor was 100 years ago or 10,000 years ago.

We are already seeing the immediate benefit of comprehensive Y testing. The research that early testers of these products provide is of immense interest to you now. While I don’t want to say that this will make Y-STR testing obsolete this is an eventual possibility. How so you say? Well let’s imagine we have a catalog of 250,000 or more Y-SNPS (at the beginning of 2014) we have 25,000 and that in those 250,000 are many surname defining SNPs. So lets say your name is Collins and the Collins DNA project has identified 14 Collins family groups each with their own identifying SNPS. One of the groups has members from the same area of VA as your Collins. So rather than take an expensive test you order a $39 Y-SNP ($18 at YSEQ.net) for that family group and voila you match! Now that SNP can take you back through your US Collins family to a Collins Family in Nothumberland, England and then back to a particular village and then perhaps back in time to its Viking extraction and so forth.  A few years ago we would not dreamed this was possible but to some extent it is already happening. And for adoptees testing and identification of private SNPS could be of utmost importance. 

HOW DOES THIS WORK

The critical YSNPS at the beginning of the Y haplotree distinguish the major branches in the letter designations A, I, G, R etc. Then each SNP below say “R” further subdivides that group. For example your current designation might be R-U106. The advantage of SNPS is that they are definitive. We can look at a SNP such as U106 and know that this mutation happened in just one man about 4800 years ago. All men that descend from that man (strictly patrilineal) must carry that SNP. All men that do not share that SNP cannot be descended directly through their Y. SNPS do not change back and forth like STRS. Here is an example from the SHELDON project.

A group of 22 SHELDON testers to date, all of whom are related (we call SHELDON Group B) are all Haplogroup R and U106. The SNP path for this group has been boxed in orange ending with SNP S15663. You can see that there is a broad subdivison at the top into M323, Z156 (aka S264) and Z301 (aka S499). Each series of new SNPS further divides the group into those that have that SNP and those that do not.

U106 Phylogenetic Tree from Eupedia

Because we have enough Big Y results for Group B SHELDON we can build a phylogenetic Tree coming forward in time. We begin with the SNP FGC62079 which is just below SNP S15663 (see above Eupedia Tree) and as you can see includes many surnames. Below it is the SNP BY35166 which to date only includes those bearing the SHELDON surname. THIS SNP then Defines SHELDON Group B! It includes both Group B Progenitors: John (13) SHELDON and Isaac (8) SHELDON (part of the Sheldon Family Association nomenclature). Those in Group B1, the Descendants of Isaac (8), have a SNP FGC74472 which is not found in descendants of John (13), thus creating a major subdivision. John (13) descendants are further separated by the SNP FGC73741. Descendants of John 1, 2, Isaac 3, Thomas 4 are positive for this SNP and descendants of his brother John 1, 2, Isaac 3, Robert are negative so we know this SNP occurred in Thomas! This is how testing can help identify branches and so SHELDONs can establish there line even if there is no paper Trail with relatively inexpensive SNP testing. Cost for a single test at YESQ.org is $18 (plus one time charge for a kit of $5). With more testing we will be able to further identify branch SNPS.

Phylogentic Tree of Group B SHELDONs

To place this in a historical context you can use the wonderful SNP Tracker to generate a map like this.

Group B SHELDON SNP Tracker Map

And SNP Tracker can also be used to create a Timeline Graph.

SNP Tracker TIMELINE GRAPH for SHELDON Group B


I give a more comprehensive example on my FGC22501 page here. Also a step by step in Lesson 15.

LESSON 15

ADDITIONAL RESOURCES

FTDNA’s white paper on the Big Y 700

The Tree of Mankind 2020 by Mike Sager from FTDNA
Greg Magoons Presentation on the Y at Igg confernce

ISOGG SNP Testing page for a visual view.
Review of new Y Products by Debbie Cruwys Kennett
On Finding Where Your Paternal Ancestor Came From Using Y DNA Results by PNGarr

Y-STR.org tools

Full Y Experimental Tree from Y Full

Big Y Matching by Roberta Estes
Y-SEQ.net New Company offering a single SNP testing service  by Debbie Cruwys Kennett
Recombination Dynamics of the T Chromosome Palindrome by Pille Hallast et al in PLOS Genetics (advanced discussion)

YSNP testing Strategy by David Dowell

Excellent video on Y SNP Testing. By John Cleary at the WDYTYA Live 2016 in Birmingham.

Genetic Genealogy Y-DNA, Ancestral Trees and Mutation Graphs

Kelly Wheaton Copyright 2020. All Rights Reserved.

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